Tears of Time - For Time Begins Anew
by the-majestic-tale
Summary: Lyra Schafer is an up-and-coming inventor in London, 1850, who dreams of the stars. Everything changes, however, with the arrival of a creature from an alien ocean, and a mysterious man in a blue box. She is pulled into a journey to the furthest reaches of the universe, but can she trust the man who walks in eternity? The one who calls himself "Doctor?" Episode 1 of TOT.
1. Lyra

Tears of Time

Episode 1

For Time Begins Anew - Part 1:

 **Hey, guys! This is my first crack at fanfiction in quite some time, so thanks for reading! This is structured similarly to an actual series of Doctor Who, with 12 episodes total - each episode will be a different story, and each story will be divided into 4-6 chapters. I've come up with some interesting ideas, so stay tuned for alien worlds, historical sagas, dabbles into some really interesting mythology, and more. Reviews are always appreciated, as I lack motivation, and they give me that little push I need to keep going. Thank you so much for checking this out, and enjoy the show!**

The lady stared up at the stars, the brilliant worlds burning and pulsing before her. As they slowly made their way across the universe, the woman fixated on the blackness that filled the gaps, and she wondered everything.

Leaning up against a rusted and rickety guardrail, Lyra Schafer saw the magnificence of the heavens revealed to her from the balcony of her 3rd story laboratory. Oftentimes, she would work long nights, nearly driven mad by the monotony of switches and lights and metal, and she would decide to rest her eyes on that which always astounded her - the nighttime sky. She could stay there for hours, contempt with letting her eyes wander from star to star, imagining what life could be out there. Only a glance at her feet beneath a black and white gown wrapped in a protective apron brought her back to reality. No matter how close she felt to the stars, the cruel realities of 1850 never seemed to end. With a despondent sigh, Lyra turned back to face the doorway to the laboratory. She pulled on the gilded handle, and was met with her life's work.

Lyra figured it was about time to make her final preparations. She pulled out her pocket watch for a quick glance - it was 9:45, almost time for her presentation. Across the laboratory, bits and pieces of every sort cluttered dusty workbenches, chalkboards were furiously marked with long sticks of chalk worn away into stubs, and candles wound down to nothing deep into the night. Vats of chemicals bubbled and fizzed, and tools of all shapes and sizes hung upon the pale walls. Sometimes, these images would haunt Lyra's dreams, yet she always found refuge in her thoughts of the stars. They were what kept her grounded, and helped her as she realized her calling - creation.

A booming thud nearly knocked the well-used wooden door at the face of the laboratory off its hinges. Lyra jumped, nearly spilling a container of potent chemicals onto her magnum opus - what her presentation was to cover. Resting on a wide workspace in front of her, a beige dropcloth coated a vaguely rectangular shape that stretched up into the rafters of the room. Lyra raced to open the door, nearly collapsing over a pile of papers resting by a desk, unable to be placed there due to clutter. In a swift yet regrettable motion, Lyra opened the door, forcefully swinging it into the adjacent wall. Outside the wall stood two men, one burly and one thin, dressed in exquisite suits and top hats. The lanky man held a thin journal and a dripping fountain pen, in preparation for what was to come. The burly man twitched his moustache, flashing a concerned glance to Lyra.

"Madame, is everything alright?" The burly man asked confusedly.

Pushing herself off of the ground, Lyra let out a nervous chuckle, stuttering over her words. "Y-y-y-yes. Everything's quite alright." she sputtered out, oblivious to the compass which became tangled in her brown hair. "You must be here to judge my acceptance into the committee. Mr. Browning? And Mr. Wilde, I presume? I apologize for the mess I've made," she continued, with a sheepish look glancing to the floor.

The burly man, Mr. Browning, gave her a stern look, replying, "Well, if your organizational skills are as good as your creations you've written to us about, there is no chance of you ever persuading us. Very well, show us what you have produced." The thin man, Mr. Wilde, looked down at his journal bitterly, writing what could only be critical thoughts.

Lyra hurried in front of the massive cloth-covered object, not even bothering to glance behind her. Her only focus was maintaining eye contact with the two men. Browning and Wilde ran a manufacturing plant not far away from Lyra's laboratory in the outskirts of London, near the river Thames. A positive impression upon the men could mean a lifetime of mass-producing her inventions, finally enabling her to make a proper living off of her passion. Lyra desperately wanted to reach out and clamp her trembling arm in place, but restrained her free arm out of fear of the two men. Doing her best to avoid stuttering, Lyra began her presentation.

"Gentlemen, as the owners of Blackstone mill, you must know how imperative proper maintenance of equipment is, particularly that it must not overheat. Overheating could create more injuries than you are liable for, and could be devastating on a wide scale. Thus, I propose a safer way to keep pressing machines and steam engines safe from overheating and collapse. She grabbed the beige cloth and ripped it towards the two men, refusing to break eye contact. Besides, what lay beneath had filled her mind for the past several months - there was no need to even look at it in order to describe it.

Revealed to the two men was a massive tank, filled nearly to the brim with water. Metallic rivets and strips held the entire tank together, and a labyrinth of tubes graced the sides of the tank, leaving the front face clear for viewing. Both men's eyes went wide - Browning's mouth gaped open in disbelief, and Wilde nearly dropped his writing utensils before coming to his senses and furiously scribbling down notes. A sprig of brown hair dropped into Lyra's face, but that was no matter; things were going much better than she ever expected.

Browning was at a loss for words. He managed to spit out, after minutes of stuttering, "H-h-h-how on earth were you able to produce this? It's utterly magnificent! Indescribable!"

With a confident smile stretched across her face, Lyra relished the looks of disbelief of the two men. She replied, "The water in the tank is rich in nutrients and elements hand-selected after weeks of testing in order to provide the best cooling. It circulates in the tubes which wrap around machinery, allowing coo-"

"I am not interested in that balderdash in the slightest!" Browning replied, "How in the world did you obtain that being? I've never seen anything like it!"

"What are you talking about?" Lyra answered, chuckling at the bewilderment of the two men. She turned to face the tank, confident in her abilities: "As you can plainly see he-"

Lyra's smile dropped. There was something there that was not present minutes ago when she covered the tank. Not a minute detail, like an extra pipe or a bubbling leak, but… something else. Staring at her from the depths of the crystalline blue waters was a cephalopod. Lyra pictured the books and articles she had read about these creatures, but none of them matched what lay before her. This one was approximately half a meter long, with white, bony spikes lining the outsides of its 12 tentacles. Large eyes pierced into Lyra's soul, and the being's near-transparent body tapered into two massive flaps beyond the head. They took up nearly all of the cephalopod's body, and Lyra could only imagined what they looked like fully extended. There was no rational explanation for how it could have entered the water-filled tank, as Lyra had not touched the tank for nearly an hour. Before then, the tank was only filled with water.

"What in the Lord's name is that?" Lyra finally managed to say. "It looks like it could be some type of squid, or mollusk, or something of that sort. But never have I seen something as bizarre as this."

Continuing to stare into the waters, Lyra noticed a slight hissing noise. She glanced around her to ensure that her compressed air tanks scattered about were all shut off completely. That was, until she noticed the bubbles trailing from the center of the tentacles. The animal, however strange it was, was _alive_ , and Lyra detected faint signs of movement. She reached her hand towards the pane of glass ahead of her, and rested her hand near the animal's tentacles. As if it was waiting for a cue, the animal sprang to life electrically. Its tentacles flared back towards its mouth, revealing a sharp, stony beak amidst a ring of spikes. But most importantly, the once transparent cephalopod glowed with a ferocity Lyra had never seen in any other animal. A rich blue light rippled through the cephalopod's body, and the massive flaps that Lyra had questioned flapped rhythmically, synchronized with the pulsing lights the animal gave off. Periods of light followed by periods of dimness repeated in a cycle, and Lyra shot back in terror.

"The creature," sputtered Lyra, "I wonder if it is trying to tell us something? Trying to communicate, perhaps?"

Browning was held captive by the majesty of the creature, something unlike any other animal on the Earth, and certainly not like any other one in London. He dug into his deep trouser pockets, scrambling for his billfold. He thrusted faded and wrinkled notes towards a startled Lyra, whose breathing was only now beginning to return to normal. "How much?" he begged, "How much for this creature? It simply must be mine!"

"I'm sorry, but I wished to sell you the tank for your factory, not this… being." Lyra carefully stated. "I cannot tell you how this creature appeared here. It's almost as if it came into the tank by itself, suddenly materializing here. In fact, from what I can observe, it appears that this creature may not have even came from this world at all!" A smile that lit up the room filled Lyra's countenance; the topic of life from other worlds was simply too good to pass up, even in formal conversation.

"I don't believe that nonsense in the slightest! Clearly, you planned this from the beginning! After all, could you imagine? Life beyond our world? There's only just stars and rocks out there! Where could one obtain the water this animal needs to thrive?" Browning punctuated, as Wilde continued his frantic scribblings and musings.

"Well, I suppose you could find it in plenty of places. Ice on Mars, lakes on the moons of Saturn, locked up in comets 'round the sun. But maybe you lot don't know all that quite yet." a charming voice with a clear scottish influence resonated from behind the three. Lyra jumped slightly, causing her heart rate to skip up and down just as it had before. There was a fourth person standing, cast in silhouette form beneath the creaking door frame. Dressed in a top hat and pristine black suit, he stepped forward, gray hairs streaking across his worn and weary face. "Of course, maybe you'll never find out where it came from! It's a shame, really. I go quite a ways back with this chap and his kind."

Browning stared down the tall stranger, and with a determined look stretched over his face, he began; "I don't care who you know, mister. I was here first, and therefore, _I_ possess all the rights to this being! That is, once Ms. Schafer here presents us with an offer for this marvelous creation."

"The tank is for sale, but the creature is not." Lyra replied, colder than ever.

"Well, if the tank is suitable for life of this form, perhaps I can search for one of these beings and house it in your brilliant casing. How much for the tank, then? A year's wages? Two years?" Browning persistently declared.

Lyra's hands began to shake. " _A year's wages?"_ Lyra thought to herself, " _more money than I've seen in my life? Can I lose this opportunity?"_

The strange, scottish man interjected once more. "Look, I gave you an offer, you two! Don't you want to know where that squishy fellow in there came from? We're talking about a living creature here, not a piece of property to be squandered over!"

The room was silent for a few, critical moments. Browning gazed upon the stranger unhappily, asserting, "Alright. I see just what you're trying to do with me. You want all of that for yourself! You're plannin' on giving her a better offer, aren't you? Well, you can't fool me!"

"Please, mister. I'm not trying to hurt you, or anyone else. I'm not trying to buy anyone out. All I'm asking is that-"

"Frankly, I don't care whatsoever what you ask!" Browning grew red in the face, and shook as he spoke to the man. "If you're trying to drive me out of this deal, consider it done! I don't need this tank or this creature anyway! I could create a million more tanks just like this if I wished, and I could search the seas of the world and find a million of these beings!"

"You've got it all wrong!" The stranger continued. "You don't understand what is in front of you, right now, wriggling around in that tank. That is all I was ever wanting to-"

"Fine! I suppose you want to cheat me out of a deal! I can make a hundred more deals far better than you can, with or without this creation!" Browning pivoted furiously towards Lyra. "Consider our deal over. I refuse to invest. Not with this man scheming and colluding against me!" He motioned for Wilde to join him, and with a final hiss in his tone, he spat out, "Good evening, Ma'am!". The two exited, as Browning swung the rickety door shut behind him, rattling the foundations of the lab.

Lyra turned from the still-vibrating door to the man in the top hat, her gaze as sharp as a sword. Tears began to well in her green eyes, and she stormed towards the man, who was pinned up against a wooden-panelled wall behind him. "My late mother and father taught me how to be a proper lady. They told me never to lay hands on a man I did not give love and consent to. As of now, I may have to make quite an exception on your behalf!"

The man was thrusted forward by his shirt collar, pulled into clear view of the woman's face. "Do you have any idea how much that money could have changed my life?" she angrily continued, "that I've been struggling so much to provide for myself? I thought I could finally make a living through my inventing, and yet you let me down in the end! You have no authority, and certainly no right, to ever set foot in this space again!"

With a tone as calm as when he appeared, the man spoke, "You're asking the wrong question."

"Excuse me?"

"I said, you're asking the wrong question. It's not, 'Do you know what that money could do for me?' No. The real question you _should_ be asking yourself is, 'What the hell is a cephalopod from the oceans of Europa doing in a laboratory in London, 1850?' You humans move past what should make you curious right away, and jump to personal gain. It's really irritating, isn't it?"

"Why can't I ask both questions? Why can't I wonder how my life could be changed by my system?"

After a moment of quiet reflection, the stranger chimed in again: "You've got it all wrong again. Your life isn't going to be changed anytime soon by that tank right there. But that cephalopod is going to transform everything you thought you knew about the universe. I do take it that you've always been fascinated by the heavens and the stars, haven't you?"

"How.. how did you know that?"

"All the clues were there really, I just put them together. And also, I saw you stargazing before those two idiots came in here." The man flashed a wide, tooth-filled smile at Lyra. "I'll be right back. Trust me, you won't miss it!"

And just like that, the man sprinted for the door, vanishing into the night. Lyra tracked him past the frost-stained windows that filled the laboratory, but she could not seem to find him for some time. Gazing down three stories, she could have sworn she saw the man break into a sprint down the street, vanishing behind a carriage passing by. She pressed her face up against the cold, icy glass, refusing to believe in what she just witnessed. " _It's probably just some drunk fellow from the tavern, going 'round banging on people's doors."_ Lyra reasoned. " _What's so special about him?"_

Lyra's brown hair fluttered up against her face, temporarily blinding her. " _I could have sworn that I closed that draft up! Not again…"_

But this was no draft.

A harmonious noise filled the room, starting faintly at first, but crescendoing to a glorious vibrance. It was a powerful noise, yet felt as weak as a man who groaned and wheezed. Lyra turned around, and realized that the source of the draft and the noise were one and the same. Atop the workspace, an object was coming into view, as if it was appearing from nothing. It eclipsed the tank and the creature - almost as if it could sense the impending object, the animal flailed its arms erratically, lights dancing over its wide fins.

Lyra was left gazing in wonder as the noise and draft stopped, and the object locked firmly into place. It was perhaps over 2 metres tall, painted a rich blue with a series of windows allowing for glances inside. Lyra had never seen anything like it before.

She peered closer to the object, a rather large blue box, and carefully studied the intricate wooden markings on the front face. Suddenly, a door swung out from the front of the box, startling Lyra and sending her to the floor below her. As she heard the crunch of a piece of glassware shattered by her clumsiness, she looked up to see the man from before reaching an arm out from within the box. "But.. how did… how… I…"

The man scoffed at her stuttering. "You think _this_ is surprising? Then do I have news for you…" He paused, and carefully considered his next words. "You've always wanted to see the stars, haven't you?"

Lyra nodded, her eyes dancing and darting around, trying to comprehend what lay before her.

"Well then, why not start now?"

"But… that's a box. That appeared out of nowhere! What does that have anything to do with a little interest of mine?"

"That cephalopod showed up out of nowhere too, and you aren't criticizing _it's_ life choices, aren't you? And besides, I think we both know that the stars aren't just a 'little' interest of yours. Look around this space!" the man shouted, "there are star maps covering the walls, I've counted no less than five globes, three telescopes, and 27 books and pamphlets about the stars and the nighttime sky. Like I said, the clues were all there. You desperately want to make things here on Earth and hopefully earn a decent living off of it, but did you see how excited you got when you realized that thing could have come from a different world entirely?"

"How long were you standing outside my workshop for? What were you even doing there in the first place?"

"That's the problem with people in general - you never get to the heart of the problem. If you must know, I was trying to shoot for Zanzibar. I was to have a lively conversation with the sultan of Omar, but I spilled my coffee on some of the controls in here. I was trying to figure out where I was, and picked up a life signal that was extraterrestrial in origin. I ran up to your flat up here, and came just in time to see your lovely space squid. But that's not important, not now at least - we have an extraterrestrial being in your run-of-the-mill laboratory, and - wait, do you live here?"

"Yes! I do live here, as a matter of fact!"

"Well, where's the bedroom? Where's the kitchen?"

"You just chastised me for not getting to the point, and now you're going off on a whim? Are you always this hypocritical? _And if you must know_ ," she continued on sardonically, "my bed is crammed back behind the bookshelf, and who really needs a kitchen when you have shelves and a wood stove? I don't exactly live like royalty, but that's none of your concern!"

The man sighed, and offered his hand out to Lyra once more. "Please, just get in here! I'm sure of all people, you'd be interested in my-"

"I'm not even sure two people could fit in that! And what on Earth did you do with my tank?"

The man's voice got quieter, as he realized how confused Lyra became. "It's… inside my…," the man hesitated, "...machine."

"Well, what does your 'machine' do? You know, other than come crashing into my life, tearing my dreams down?" She became just as red in the face as Browning had become earlier.

"Again, you're missing the point! Grab my hand, I'll pull you up here. Unfortunately, I don't think I can get her much lower…"

"Her? Why should I go with you in that thing?"

"Yes, it will all make sense in due time." The man gripped Lyra's hand firmly, and pulled her up to the workspace where the machine rested. Lyra thought for a moment that she should have resisted more, but something deep inside of her motivated her to keep going. "Follow me." And just like that, the man vanished into the box. " _He couldn't have gone far,"_ Lyra thought, " _Maybe two feet?"_

"Is this what you do? Find people and confound them to no end? She yelled into the blackness ahead of her, her voice echoing into the distance. She stormed forwards, angrily stepping forward into the darkness, one step, two steps, three steps, four steps, five steps. " _Wait, that can't be right,"_ she pondered, " _this box is less than a meter wide. Then how can I keep moving forwards?"_

The door slammed shut behind her, and the only light visible seeped in through the front windows. But where were the side windows she had seen earlier.

"Confound people? Not exactly."

And then, Lyra's surroundings burned brilliantly, brought to life with light. She wasn't standing in a mere box - she was almost two meters away from the door. The man stood before her, next to her…

The tank, cephalopod and all, rested under the crimson and gold lights that shined from all corners. It was then that the true magnificence of this space was revealed to her. What once seemed too cramped for even two people could hold a hundred, perhaps more. She spotted bookshelves, chalkboards, and many gadgets and machines she could never even dream of. And central to it all was a powerful column, with tiles that held levers, buttons, switches, and fabulous yet indescribable controls. Moving her eyes up the column, Lyra noted the red and yellow lights in the center of a clear framework, and massive rotating wheels that came to life at the top. It was not just a machine. It felt alive to Lyra, as if it the metal floors she stood on flexed while the machine took a breath.

"You said you wanted to see the heavens. This is my ship, and it will take you there and beyond. Some call it a bringer of hope, while others call it the most dangerous craft in the universe." The man smiled as he did earlier at Lyra. "I prefer to call it something else - TARDIS."

"What is it? Does it have some type of observatory? Did, did you build this? How is it-"

"Why must you ask so many questions? Can't you just skip to 'It's bigger on the inside than the outside?' Most people would have gotten there by now at least. I can assure you, you will get answers in due time, but first, I think we really need to get moving. Otherwise, who knows what'll happen to your squishy young acquaintance here," the man said, gesturing towards the cephalopod, who was no longer blue. Instead, its broad sails unfurled and changed to vibrant reds and yellows, matching the lights that flashed and glared inside. "So, whadda you say? Trip of a lifetime?"

Too struck with wonder to speak eloquently, Lyra shared the same smile as the man before her and said, "You can pilot this ship? Where to?"

"Anywhere in the universe and back, through anything time throws at me." The man rested his hand on a silver lever, stuck in an upright position underneath the rotors above. "I am no mortal. I'm a Time Lord. Extraterrestrial. I have more in common with that fellow in the tank over there than you. To you, that may not mean much, but to me, it means everything. I walk in eternity, unconstrained by the rules of the universe." He smiled even brighter at her. "Well, maybe not _all_ the rules, but who cares? I travel to everything that ever could happen, and everything that would happen, because in those could haves and would haves, that is where history is made. You could have made that deal with little regard for our little friend here. But you did something different - you wondered. You imagined what could have happened. And if we're being serious here," he continued, "I think you took pity on it. You said earlier about what your late parents taught you. Perhaps you simply couldn't bare leaving it alone, just as you've _felt_ alone in your workshop. But you can't see the universe in your books and studies. The universe is calling to you, Miss… I never really got your name."

"Miss Schafer. Lyra, if you want to know."

"Welcome aboard, Lyra. Shall we begin, perhaps with this fellow here? I've encountered his species before, on Europa, one of Jupiter's moons." With that, he pulled the lever he rested his hand on earlier, sending all of the lights around with a blur. The same noise that had filled the workshop earlier rang through the caverns of the machine. Lyra tried to take it all in, but she knew that she could not. Soon after, the man lifted the lever up once again, bringing the machine to a halt.

"I'm the Doctor, by the way - people just call me that. Not an actual doctor, so don't go passing out much, alright? That's all I'm asking."

"People really call you that? Just, 'Doctor'?"

"It started ages ago, and they've never really stopped. But that doesn't matter now. Lyra, go back to the door, and open it up for me, would you?"

Confused by the request, Lyra turned around, grabbed the door handle, and pulled the door open. It was then that she knew why the mysterious Doctor had asked her for this. Below her, she saw that astounding blue marble, the Earth. Winds roared below, ocean waves pounded, and she could almost feel the majesty of the planet spinning, hurtling itself through spacetime. And beyond that, was the barren and cratered moon, and innumerable stars. It seemed so tranquil to her.

"To answer your question from earlier, no. This place is not an observatory. It doesn't need one, when you can see all of creation from the doorstep. Welcome to the universe, Lyra."

Lyra stared up at the stars, the brilliant worlds burning and pulsing before her. As they slowly made their way across the universe, the woman fixated on the blackness that filled the gaps, and just as she had done on the balcony not less than an hour ago, she wondered.

Lyra wondered everything.


	2. Kamkora

Tears of Time

Episode 1

For Time Begins Anew - Part 2:

Lyra still attempted to wrap her head around the enormity of the past hour - one moment, she was preparing for a new life on Earth. The next, she began preparing for a life beyond the stars. She still couldn't comprehend how something could be bigger on the inside than it could be on the outside, even after The Doctor's fruitless attempts to explain it to her. She was still focused on The Doctor's original goal, however - to return the lonesome cephalopod to its homeworld.

"Europa? Why would there be anything alive there?" Lyra smirked as she hovered her hands over the silver console in front of her. She could never quite resist such intricate machines, with countless wirings and inputs.

"The entire undersea ecosystem established there is all thanks to the starliner _Calypso_. It crashed about 20,000 years ago, relative to your timeline, that is."

"Starliner?"

"Big spacecraft - kilometres long. Get used to big, sciency words that you don't really understand. That's what happens when you travel across the universe. Anyways, _Calypso_ sailed the stars for thousands of years, until it crashed into Europa's ocean."

And that's important for what reason?"

The Doctor raised his eyebrows and grinned at Lyra as he calmly moved around the TARDIS console, flipping switches and pulling levers. "A lot can happen in 20,000 years. Polyps native to

Europa's ice-locked oceans began to build colonies all over the ship, eventually forming a massive coral reef structure. That structure allowed an entire food chain to develop, starting with small animals, and with your friend here, in your tank." He ran over to the tank for a brief moment and rested his hand on the blue tinted glass. Behind it, the cephalopod ran a series of blue and red lights through its sails, and its tentacles began to twitch.

"I've met these creatures before. Kamkora, I believe they're called. Similar to the cuttlefish you have in the oceans on Earth, but these ones are much more incredible."

"How so?"

"The spinning lights and rotors of the ship came to a halt. The Doctor made sure to perform one last action - winding a nearby crank several times - before thrusting open the doors to reveal an alien world.

"See for yourself." The Doctor said with a grin. "I've extended the TARDIS's air shields - you'll be able to breathe comfortably for a 3 metre radius."

"What happens if I go outside that zone?"

"I would prefer that your first trip in my time machine doesn't end with you drowning in a methane ocean, so please don't." The Doctor flashed a grim smile at Lyra, who grew more perplexed at this man, and more importantly, his words.

"I never thought that I would travel this far in my entire life. How far away are we from Earth?" Lyra pondered.

"More than 600 million kilometres, further than anyone from your time has gone before. There's an alien moon out there - you've always wanted to run freely through the universe, now run out there!"

Lyra's look of uncertainty turned to one of sheer excitement and childlike wonder as she moved to face the open doors. The crystal clear blue waters danced in front of her, atop a black sand bed. She took quick yet hasty steps towards the door, took a deep breath, and let her foot touch the alien terrain. Her shoes, worn down by years of decay and constant pacing in her lab, sunk into the fine-grained sand beneath her. Before her was a gargantuan reef system, different shades of red, orange and yellow. She understood what the Doctor meant by a starship crashing there - she could discern windows, bolts, rivets, sheets of metal poking out of the jagged coral branches. "It's… it's beautiful", Lyra confessed, "It must be the most beautiful of its type in all of space." She continued to step out, her feet diving deep into the soft basin below.

The Doctor scoffed at this mention. "Clearly you haven't been to the coral reefs of Wisconsin."

"Wisconsin? As in Wisconsin in the United States? There's a reef there?"

"No, I'm obviously referring to space-Wisconsin. _Yes_ , Wisconsin in the United States! Well, not in Wisconsin as you know it. Like I said, just as a lot can happen in 20,000 years, give Wisconsin 450 million years, and it's not that hard to find oddities."

"Is there a space-Wisconsin? We should give that place a visit afterwards."

"No, there is no space-Wisconsin!" The Doctor replied, irritatedly. "Keep looking - there's more to the reef than just coral, you know."

The Doctor was correct. Just beyond the edge of the _Calypso_ lay ghastly white tubes with red tips that ebbed and flowed with the current. At the foot of the wreck were writhing worms and twelve-legged crabs with iridescent shells. And all around the reef were fern-like plants, nearly 3 meters tall. They were colored a striking maroon, and they were home to crusts of barnacles. "Are there any fish here?" Lyra pondered.

"No, at least not yet - no vertebrates live here. Life is in its infancy here. Silicon-based life forms, crawling out of the depths of the ocean. But for now, nothing lives above the ice caps."

Lyra looked at him, puzzled. "Are you sure? There must be something truly massive here - perhaps a top predator?"

"I wouldn't think so, Lyra. This is a rather new ecosystem, so there hasn't been much time for evolution to run its course and create something that large.

"Then what," Lyra exclaimed, pointing her arm towards a large moving shape. "is that enormous creature?"

"That is not _one_ creature. It's a swarm of hundreds of smaller creatures. Kamkora!"

A flock of the cuttlefish-like creatures, came into view. Each individual possessed the same luminescent qualities that the original specimen had, and the end result was a breathtaking array of color and light. Reds, blues, purples, colors of all types flashed erratically, and each passing animal was different from any others that surrounded it. Hundreds and hundreds of them passed by the duo, gently curving around the established air shield. Lyra was astonished that the animals moved so fluidly, so elegantly - almost as if they couldn't exist. She constantly had to remind herself that this was an alien world, and as such, the inhabitants would perhaps be equally bizarre. "What are they doing, moving around in such a large flock?" Lyra inquired, as the Kamkora continued past them in a blur, colors blending together effortlessly.

"They're migrating. This is where they spend half of the year - half of Europa's year, of course - coming here to feed on the nutrient-rich smoke of the oceanic vents here. Back there!"

The Doctor pointed behind the TARDIS, and Lyra hurried over, astounded that they could be fully underwater, yet the air shield kept them breathing and completely dry. In front of her were three massive mounds of earth, spewing black, dense smoke into the water above. As she followed the wisps and their journey towards the surface, she noticed the massive ice caps that locked in the alien sea. She could see the herd of Kamkora moving closer to the smokers, when the movement stopped entirely.

The animals lined up around the smokers, each one taking a different position along the rising column of smoke and gas. Lyra could discern the bony spines that lined each tentacle of every Kamkora. She wondered what the purpose of the spikes was, and then she saw the answer. Out of each spike shot a thin, feather-like appendage, about half the length of one tentacle. Most of the cephalopods became instantly covered in these structures, and each animal moved its tentacles into the black fog.

"Here is where the Kamkora's feeding strategy comes into play. These fellows are masters at chemosynthesis - the animals that live in the deepest, blackest parts of the sea on Earth can perform this same feat. They don't need to eat other mobile animals, because they feed on the nutrients and bacteria in the vents, remember? It all gets trapped in the feathery structures, all the food a Kamkora could need." The Doctor paused, and watched with Lyra as one by one, the animals moved their feathery tentacles towards their beaks, stripping each one of nutrients and microscopic organisms. "Once they've entered the beak, the nutrients and bacteria are used to power the Kamkora. They are remarkably simple yet intelligent creatures, so most of the energy goes to locomotion, and the main purpose of the brain - coordinating light."

One of the Kamkora came right in front of the two, between the air shield and the black smoker. Its fins dazzled an incredible green and yellow, and blue waves crested up its tentacles and body. The Doctor continued his discussion, "Tiny electrical impulses travel all throughout its body, widening sacs filled with pigment. Each Kamkora has a different set of pigments, and they've learned to read each other - that's how they talk to one another". The Kamkora in front of them came across another one, this one flashing purple and blue. Tentacles shifted, and each cephalopods' fins became as red as blood.

"This is the true majesty of the universe. Worlds and beings beyond your wildest imagination. Fantasy becomes a reality." The Doctor mused, as Lyra stepped closer to the edge of the TARDIS's air pocket. With a slight trepidation, she reached up towards the two Kamkora, now glowing furiously red, tentacles drawn all the way back.

Lyra touched the border separating air from water, and was captivated by the trickling and rippling of waves coming from her hand. Going further, she pushed her hand up into the salty current, feeling the weight of the alien world. One of the Kamkora's tentacles gently brushed up against Lyra's fingers, the bony denticulations and smooth surface delighting her. She was interrupted from her fascination by a grave tone from behind her.

"That's not good. That is very, very, not good."

Lyra jerked her hand back, creating larger ripples that startled the two Kamkora. "What's not good?"

"That!" The Doctor was standing at the opposite edge of the air pocket, pointing at one creature in particular. Lyra rushed over to see it - another Kamkora, illuminated orange and blue, but its tentacles were neither color. They had become completely black.

"Why's it so dark? Is that supposed to happen?"

"No. It's not. If it were, only the tentacles would be black. But look at how the color is spreading." The dark pigment was slowly taking over the entire creature's body, and the more the pigment spread, the less the Kamkora moved. Soon, its eyes were overtaken, and all it could do was helplessly sputter its fins and flash blinking lights. But it was no use. All traces of electrical blue and orange color vanished shortly after. In a span of minutes, the entire animal was caked in black, and all movement stopped, save for a calm drift to the seabed. It lay petrified, disturbed only by the slightest currents. One of its tentacles snapped off of the body, coming to rest parallel with the black sand.

"Doctor, is it... dead?"

"I'm not sure, but for all intensive purposes, yes." He pulled out a slender silver and blue object from his suit jacket pocket. Turning a chrome dial on its side gently, he pointed the device at the deceased Kamkora, and a green light and a metallic hissing noise resonated.

"What is that thing?"

"Sonic screwdriver. It's a screwdriver, and it's sonic. Think of a swiss army knife, but for the universe. But I'll tell you what - I've got good news and bad news. Good news is, that animal is definitely dead."

"How is that good news?" Lyra interjected.

"Because it means that I was right earlier! Anyways, the bad news is that I can't tell what killed it. It's a shame, really. I've seen these guys before, back when the reef was young and the sand was white." The Doctor then closely examined his screwdriver, checking for anything of importance. "Normally, my screwdriver can detect nearly any chemical trace, but if whatever killed this thing was indeed chemical, it must be too small to detect."

"Doctor-"

"It would have to be something that could render the Kamkora immobile, and shut off its light coordination properties. It-"

"Doctor-"

"It had to be something species-specific, considering that the coral hasn't died yet-"

"Doctor!"

"I need to think! What would shut down something completely, and affect only the Kamkora?"

"Doctor!" Lyra began, "You said that when you last came here, the sand was _white_ , when the reef was young."

"Your point is?"

"Then why, pray tell, is the seabed completely black?" She continued, waving her arm across the seabed. She bent over and scooped up a handful of the foreign matter. In an instant, her face no longer expressed curiosity, but understanding. "I think I have an explanation - this has been going on for a very long time indeed."

The Doctor's eyes widened at the thought of this. "You may be on to something! If this has been repeating for thousands of years, migration cycles ending in this, then how do we know that the sand is really sand at all?" The Doctor pointed his screwdriver at the seafloor, and pulsed the lights on again. Almost immediately, the sands came to life in brilliant colors of red, green, blue, and many many more.

"Is that what I think it is?" Lyra asked, her voice beginning to strain at the implications of the light.

"Unfortunately, yes. Pigment sacs preserved in the sand, from decaying, petrified organisms. I've just activated them with an energy field from my trusty screwdriver, here! Because this - this is not sand at all, but the petrified bodies of Kamkora, eroded into dust after thousands of years. Lyra, we're not dealing with just one single death here. This could be an extinction-level event! But what caused it? Some type of potent chemical, neurotoxin, or other incredibly small substance? Where did it come from?"

"Doctor, what did you say earlier about that starliner?"

"What does that have to do with this?"

"You said that a starliner called _Calypso_ crashed here some time ago, and the reef was constructed around the wreck. Maybe this isn't a natural toxin we're observing, but-"

"An artificial one, locked up in the reef!" The Doctor excitedly concluded. "It all makes sense! Consider the oil from a starliner - a technologically advanced species could theoretically construct oils and fluids made of very small particles. And the Kamkora are-"

"They are chemosynthetic, as you told me? Then perhaps this toxin interferes with the feeding process, starving it to death."

"No, this was quick-acting. Kamkora have tentacles filled with chemoreceptors that transmit signals to its brain. If this oil is to blame, then it clogs up the receptors, acting as a neurotoxin, and sends harmful, artificial waste products up to its brain, which controls what?"

Lyra suddenly realized what The Doctor was saying: "Locomotion and color. If it interfered with the brain, it would stop producing color and turn black, and stop moving and fall to the ground. That's it!"

The Doctor grinned, and finished Lyra's words. "Both of those functions are inhibited, and I happen to know that whoever built _Calypso_ used state-of-the-art nanocarbon oils! They would lock up in rigid formations as they overtook each Kamkora, petrifying them completely!"

"Doctor, I think we may need to be moving a tad bit quicker…" Lyra gripped The Doctor's shoulders and spun him around, until he faced the other side of the air pocket. Dozens of Kamkora had blackened tentacles - some only at the tips, some almost up to the eyes. One by one, each of the affected animals stopped moving, and began to rain down to the sea floor. Petrified bodies piled up, first one, then two, then ten. The survivors flashed their fin lights rapidly, moving away quickly from the danger. "Doctor! Whatever you're planning on doing, I would recommend that you do it quickly! Let's just hop into your box, find a solution, travel back in time to _before_ we arrived, and save the Kamkora? That would solve all of our problems!"

The Doctor's smile dropped. "Time doesn't work like that. You can't just go anywhere and everywhere, you know." he replied, "If we stopped the Kamkora from dying _before_ we arrived, we wouldn't have any need to travel back and stop them from dying in the first place. It's called a paradox, and I've dealt with far too many of those. It's like meeting yourself from the past, or something like that. Avoid it at all costs, because you never know what could happen."

"So, what are we supposed to do now?"

The Doctor remained silent for several moments, his breathing growing more heavy as time trudged on. Finally, he spoke, "I know what we have to do, and more importantly, where we have to go. This is absolutely not going to be good…" He paused for another moment of contemplation. He jerked quickly and snapped his fingers, springing the TARDIS doors to life. "Lyra, into the TARDIS."

"Where are we going?"

"It's about time I talk to an old friend of mine. He can help us out, possibly."

"I thought you said this wasn't going to be good. What's wrong with your old friend?"

"Travelling with me isn't always like this, seeing space squids and crystalline underwater reefs. There are monsters. There are unfathomable evils in the cosmos. Species struggling for absolute power and nightmarish control. I am about to come face to face with one of those evils, in the darkest dredges of the cosmos - Lyra, get inside!"

Lyra reluctantly went into the TARDIS, and The Doctor followed closely in a sprint. The doors slammed shut behind the two, and The Doctor furiously manipulated the controls, sending the TARDIS adrift into spacetime.

"Hello there, Squiddly. Is that a good name for you? Squiddly?" Lyra peered into the tank holding the hopefully unaffected Kamkora. It's sail-like fins dragged and it only glowed faintly, but no signs of blackness were present in the tank. It was as if it could sense it was being separated from its world - or worse, that the other Kamkora were dying. "You don't look that bad! Even if you look a bit odd, it's still far better than getting turned into space dust." Lyra softly chuckled, oblivious to The Doctor's distress. He wiped beads of sweat off of his forehead with his suit jacket, and tossed his hat aside, before glancing at Lyra.

"You named it?" The Doctor said, perplexed by Lyra's actions.

"I'm not the best at naming things, you know. You would think that I would get better over time as I invented more devices, but I-"

"That's not what I'm worried about. I'm concerned that you named it at all - don't get attached to it."

"I'm not getting attached to it! If anyone could get attached to an extraterrestrial squid, I have no doubt that it would be you!" Lyra retorted playfully.

"At least he'll keep you company while I'm away, Lyra."

"Away? What is that supposed to mean?"

"It means that we're entering dangerous territory, and I won't let you loose among some of the most menacing races of the cosmos. I'm going to get the antidote for the leaking fluids in the _Calypso,_ and the only way I know how to do that is to send the TARDIS into the 52nd century."

"How is _that_ going to save the Kamkora?"

"I'm going to save them by being extraordinarily clever. I tend to do that a lot, so if you pick up on it now, it will really help you in the long run." The Doctor stopped moving around the TARDIS, and the lights and rotors came to a halt, as they had upon arrival in Europa's sea.

"Why can't I go with you? If I can handle space cephalopods, I am more than certain I can handle deep space, or whatever it is that you're getting yourself into!"

"My box, my rules! Stay in here, keep an eye on 'Squiddly', or whatever the hell you decide to name him, and don't come looking for me I'm sorry, but you won't stand a chance in Contrapasso!"

And with that, The Doctor exited, sealing the doors behind him. He quietly pondered if he had said too much already.


	3. Tempest

Tears of Time

Episode 1

For Time Begins Anew - Part 3

The Doctor stood before the gateway to hell.

He was about to enter Contrapasso: the cesspool of the universe, a beacon of destruction on the planet Denosive. He had traveled an indescribable distance to reach the cratered, dead planet.

Well, _almost_ dead.

Behind him rested the TARDIS, nestled securely underneath a matrix of steel and steam, a framework built by the inhabitants of the world. The Doctor remembered them fondly. " _Denosivians. Lovely bunch, really - I remember the first time I heard of them. They were part of legends and bedtime stories back on Gallifrey; those were the days. Masters of technology and design, even more so than the Time Lords. No wonder they could build starliners..."_

Now, The Doctor stood in front of a massive set of steel doors preparing himself to enter the presence of countless alien races. He dared not risk Lyra going into a world of alien criminal gangs, rogue factions, and would-be Gods. One deadly race would already prove difficult. Five hundred deadly races, however?

There wasn't any doubt in The Doctor's mind about his decision, and he gripped the silver handle nearest to him. With a swift jerk, the door slowly creaked open, bits of dust dancing in the stray light beams originating from Denosive's white dwarf star.

"I'll tell you what - I was not expecting that."

There was no commotion or chatter. No clinking of drink glasses, no weapons, no music. There weren't five hundred deadly races here, let alone five hundred peaceful ones. No life, save for The Doctor, could be found Contrapasso.

"Come on!" The Doctor shouted, throwing his hands in the air as the door slammed shut behind him. "I didn't travel to the edge of the universe, just for me to find _nothing!_ " He angrily continued to move forward as he muttered under his breath, "Anything would be better than this wreck - I should have gone to space-Wisconsin instead!"

From the dark depths of the grand hall that unveiled itself, the _click-click-click_ of spiny legs on the hard marble floors echoed. Creaks and clanks resonated through the thin air, accompanying a slow hissing. Slowly, The Doctor turned around, cautious of whatever lay waiting for him in the shadows.

"...I have a feeling that I may have spoken too soon..."

* * *

 _The wise man cavorts through our domain, our kingdom of the dying sun. As we scuttle past the fleeting shadows, he comes into view._

 _Interesting._

 _Perhaps this man will be different from the others..._

 _No._

 _He was never wise to begin with. His trespassing is foolish and irresponsible._

 _We pluck the intricate fibers of spacetime that fill our minds, hoping to form an image of he who stands before us, the man who stands unafraid in the face of evil. The vastness of all that is, all that was, and all that will be flashes before our unblinking eyes, as we extract and process._

 _Yes, yes. It is all clear to us. We now know who he is._

 _He can run and run and run, but he will never outrun the ticking of time itself._

 _All must obey the laws of the cosmos._

 _All must succumb to the Contrapasso, at the end of the age._

 _Even the Time Lord._

* * *

"Squiddly? You better not tell The Doctor about this. Do you promise?"

The cephalopod flickered the lights on its two fins bright yellow.

"I take it that those lights mean, ' _Yes, Lyra, I won't tell The Doctor a thing!'_ "

Lyra left 'Squiddly' by himself in the tank as she covetously investigated the TARDIS's controls. She simply couldn't resist the chance of wandering around a time machine to see what made it tick. " _An actual time machine!"_ Lyra thought, " _How fortunate am I to see this? I'm sure The Doctor won't mind. He seems to be just as curious a person as I am!"_ The trouble with Lyra was that she could never seem to stand still for one moment: she always had to be pacing about and asking questions.

Beneath her hands, the silver and gold console framework beckoned, crying out to her. Dials, levers, buttons, and lights - of course, Lyra had no clue what any of them were for.

"Let's see… I do believe that The Doctor pressed this button to open and close the doors earlier," she whispered to herself. Her pointer finger of her left hand danced over a gold, circular button with a chrome border. Although she knew there was no one else with her, some irrational fear that 'Squiddly' could understand her lingered in her mind. Her judgement told her not to push it, but that intricate, burning desire to know what lay outside the doors ensnared her entire being; she pushed the button.

Almost immediately afterwards, the bright white and yellow lights surrounding the ship turned blood-red, and a powerful siren blared out in response. Lyra swore she could feel the ground beneath her feet shifting and turning.

"Which button was it?" Lyra cried out, desperately scanning the console, as the Kamkora flared bolts of orange and red light that mimicked the tumultuous state of the TARDIS. "This one?" She exclaimed, pressing the circular button for a second time.

The blaring stopped, and the red lights reverted to their original colors. Sighing heavily, Lyra slumped back behind the console, her hair in tatters. With a small chuckle, she turned to the holding tank: "I'm sorry about that, Squiddly. I hope you are not too badly shaken by that!"

Perhaps The Doctor was correct in his earlier judgement of Lyra - that she took pity on the Kamkora. If so, then she certainly felt pity for it in that moment. Backing away cautiously from the console, she sat down next to the tank, sharing a gentle smile with its inhabitant.

"Are you lonely, Squiddly? I understand if you do - but don't worry about a single thing. The Doctor will make things better, and you will be back home again." She sighed, and while she counted the holes that punctuated the metal flooring of the TARDIS, Lyra grew softer. "I know how it feels to be abandoned, left alone. It happened to me once, as well." She paused, considering how to tell the rest. My mother and father perished in a great fire when I was only twelve years old. I had no brothers or sisters, and I had no other relatives nearby to care for me. I was forced to live on my own for the first time in my life, and it broke my heart. It was around that time that I found solace, a sense of belonging, in the stars above." The squid did not respond, but deep inside, Lyra could sense that her words held a deeper meaning - if not for the squid, then for herself.

Lyra sat in silence next to the watery capsule, contemplating her next words. "Not long after, I decided to begin tinkering and toying with whatever scraps and rubbish I found around me. Soon, I worked my way up to a full workshop, the one you visited not too long ago. I wasn't ever sure of where I wanted to go in life, what I would do with my time. To this day, I still have many apprehensions about what tomorrow holds." She turned one last time to face the Kamkora. "Soon enough, you will be living life the way it was meant to be." Another smile brightened her rosy face. "What do you say? Shall we try to see how the doors open again?"

She didn't need a response from the Kamkora. She bolted up from her seat, dusted off her dress, and went back to work scanning the console for answers.

* * *

"Hello? Anybody home? Who are you, and what happened to the Denosivians?" The Doctor cried into the shadows.

" _We… are might beyond measure…."_ something deep within the shadows replied, chilling The Doctor to the bone. Its voice was soothing yet venomous, confounding The Doctor. " _We… are the lifeblood of the universe… the bringers of both peace and destruction..."_

"It would really be useful if you stopped with the epithets," The Doctor croaked out amidst his apprehensions. "I asked who you were, not who you _think_ you are. Who are you, and what do you know about the native Denosives?"

" _Have you not heard of the mighty Tempest which rendered Denosive barren?"_

"What Tempest?"

" _Rain of fire poured from an opening in the cosmos, destroying all life on Denosive… it was in that same Tempest that we arrived on the dead world…"_

"So, what you're saying, is that _you_ killed the Denosivians?"

" _You are correct… we are Tempest..."_

"That's your name? Tempest?"

" _We were assigned that name by the Denosivians… once our fires began to burn anew…"_

"Burn anew? Are you saying that you've done this before?" The Doctor bellowed.

" _Our fires burned first at the origin of all that ever was… we carved the laws of reality into the newborn flesh of spacetime… our handiwork is seen in every anomaly throughout the multiverse... we created, and we will destroy..."_ The entity moved closer and closer, the _click-click-click_ of the enemy growing louder on the battered and cracked stone floor.

"Here's a question for you, Tempest, or whatever it is that you call yourself! If you pride yourself on being so powerful, then why is your only territory here on Denosive? Surely, if you had as much power as you said you did, you would have taken more planets, systems, galaxies even, by now!" It was then that The Doctor noticed a second noise, one that he had neglected long ago. In addition to the cold, reptilian voice that addressed him and the clicking of the Tempest's body along the ground, the faint clacking and rustling of metallic chains was present.

"Of course! You never took over this planet at all! _You were imprisoned on it!_ "

" _We were taken here forcefully, from the end of the universe, blazing down from heaven in a ball of flame… the Contrapasso remained, but its inhabitants were destroyed..."_

"No… that's not right… you don't just destroy five hundred species just like that!

" _We had no need to… members of the five hundred worlds destroyed themselves in the confusion… the Contrapasso was chosen as our prison… tell us… why do you seek the Denosivians, a dead race?"_

"To be fair, I didn't know they were dead at the time. You surely know that they were monumental architects - they're the reason your prison still stands to this day. I hoped to seek out the designer of the ancient starliner _Calypso_ , and propose a request."

" _The Denosivians are of no use to you now… we provide freely now…"_

"Why should I trust you? You've destroyed an entire world, and killed millions."

" _The same can be said of you… Time Lord of Gallifrey..."_

The Doctor froze. His muscles locked up and his breathing began to hasten. "How… how do you know who I am? I haven't told you anything about myself!"

" _We know you the same way you know us… you observe us in the physical realm, but we observe you across all of your life… nothing escapes our watchful eye in the end…"_

The clicking and clunking noises accelerated. Out of the shadows came an abomination - a serpentine body propelled the massive being forward into the light. Its entire body was frozen in a moment of decay; its green and black scales had been peeled and withered. It did not seem alive, but rather, more like a ragged carcass. The creature's upper body was even more disturbing to the Time Lord; several humanoid faces surrounded one central face. The Doctor did not recognize that the faces were humanoid right away, as they were warped and distorted, with peeling black skin and black blood dripping down open gashes in the chest. Attached to either side of the entity were massive silver chains that weighed down the creature's sickly, pale legs, tipped with thousands of miniature spines - the source of the clicking The Doctor had noticed earlier. The entire body had to be at least 10 meters tall, reaching the rafters of the Contrapasso with ease. Taking a cautious step back, The Doctor realized that this wasn't even half of the Tempest - the rest was still wrapped in chains, covered in a dark, shadowy shroud.

And then, the central face began to twitch, accompanied by the Tempest's crisp but malicious voice.

" _Present your request, and if you prove to be trustworthy, it will be granted to you. Tread lightly on sovereign ground..."_

" _...Doctor…"_


	4. Covenant

Tears of Time

Episode 1

For Time Begins Anew - Part 4

 _"_ _Present your request…"_

The Doctor was at a loss for words. _"If this… creature… can truly see through time,"_ he reasoned, _"then can I do anything they won't see coming?"_ He recalled his earlier words to Lyra - he would save the Kamkora by being extraordinarily clever.

Fortunately, being clever was something The Doctor happened to be very, very good at.

"Kamkora. If you really are what you say you are, then you know who they are. Let's see what you've got!"

 _"_ _We are familiar with the Kamkora… the underwater creatures of Europa… Doctor, present your request…"_

"The silicon coral reef structure under Europa's ocean is built on the wreck of the starliner _Calypso,_ as I'm sure you're aware of, what with your magical time powers and whatnot," quipped The Doctor. "The Denosivians built the starliner, which is now leaking nano-hydrocarbon oils into the water. Those oils interfere with the Kamkora's feeding, and they block the electrical signals to the brain. And as a result, the Kamkora have been slowly dying over a period of thousands of years. I wanted to ask the Denosivians for assistance, but I think I overshot just a tad. Don't you think?"

 _"_ _What is the significance of this, Doctor?"_

"I happen to know that the Denosivians kept reserves of an cleaning agent of sorts to this oil, to clean up oil spills and factories. I don't think it's unreasonable to think that I could use it to clear out the oil, and use it as an antidote to keep the rest of the Kamkora from dying. There! Is that good enough for you?"

 _"_ _You request our help in sparing such insignificant creatures…. What benefit is there in such an action?"_

"You of all people should understand this! If you can truly peer into the depths of spacetime, then you tell me!" The Doctor shouted. "Actually, no, don't tell me. You're just going to jumble it all up and spout more poetic nonsense. To someone like you, _everything_ must seem insignificant, and _everything_ must revolve around what you can gain, what you can plunder and pillage from others - be that myself, the Kamkora, or the Denosivians! Thus, you cannot possibly comprehend why I do what I do. _I_ look at the world and have compassion for those who are less fortunate than I, whereas you've been imprisoned _for_ destroying those less fortunate than you! The Kamkora are not just cephalopods! They're living creatures, with complex rituals and family groups! You cannot alienate them just because they don't align with your presumptions! So, are you going to give me the antidote, or not?!"

 _"…_ _your humility impresses us, Doctor… caring for beings so far below you… we will grant your request…"_

"Great. That's perfectly good and all, but I'm much more interested in _how._ _How_ are you going to produce an antidote on a dead planet? You said earlier that you 'provide freely', so how are you able to do that? And don't give me any more of that spacetime nonsense, I'm getting sick of that."

 _"_ _We are all that was and all that is… we are the spawn of nightmares… we peer into time's eyes, and retrieve what is necessary…"_

"That really doesn't answer my question! _Show_ me how you do it!" The Doctor roared. "I've seen many beings throughout my travels through time who all have proclaimed that they are supreme over all others – Omega, Trickster, Sutekh, Valeyard! What makes you different from all of them? How do I know that you really are who you say you are?"

 _"_ _You have seen our immense power… how else would we know of who_ you _are, without ever once seeing you?"_

"That is a very valid point, but you have to realize that I'm a Time Lord! A flesh-and-blood Gallifreyan! I see through time just as you do! I see fixed points and flux points, paradoxes, and curves and bends and gashes in spacetime! And I certainly know that you cannot 'pull on the fibers of spacetime' and suddenly produce the antidote! Time isn't like a magic wand that you can keep waving, until whatever you want appears before your eyes!"

 _"_ _Perhaps… but there is a simpler explanation for our abilities…"_

"Oh, really? Then why don't you tell me!"

 _"_ _No… tell us, Doctor… who imprisoned us?"_

"What does that have to do with anything?"

 _"_ _Who imprisoned us?"_

"I don't know! Not when you keep talking like that!" The Doctor paused, and with a sigh, began to reason. "It had to be someone on par with you in terms of abilities, anyone below you wouldn't be able to subdue you and send you across the universe. You said you were shot to Denosive from the end of the universe, so it must have been extraordinarily advanced, lasting from the beginning of the universe to the very end. And if they imprisoned you, you must have posed a threat…"

The Doctor stopped.

"I know who imprisoned you."

 _"_ _Then tell us…"_

"…the Time Lords sent you here!"

 _"_ _You are correct… we take pride in the terror, the horror that we unleashed on the Time Lords of Gallifrey, so very long ago… we relish in the screams, the cries of the damned."_

The Doctor's hands balled into white-knuckled fists, as he grew more and more disconcerted. "That's not right… there were very few races in the universe that the Time Lords feared! If you really were such a threat to the Time Lords, then why don't I recognize you? Why have I never heard of the Tempest before?"

 _"_ _This is not our true form… nor is the Tempest our true name… now, observe the powers that terrorized your people!"_

Between the Tempest and the Time Lord, crackling golden sparks pierced through the shadows. The outline of a golden, sputtering circle illuminated The Doctor's face, and the inside of the circle was filled in with a vibrant yellow. Soon enough, The Doctor realized that this was no simple circle. He began to recognize familiar figures – the TARDIS console, the Kamkora Tank… and Lyra!"

"What are you doing to the TARDIS?"

 _"_ _We are linking with it, connecting with it… soon, you will talk with your associates… and they too will experience our might…"_

The Doctor could feel both of his hearts pounding in his chest. He felt a primal urge inside of him to scream, yet no sound escaped his lips. He began to believe that the Tempest could have frozen him in place, by means of some unknown power. He then understood that his own fear was what locked him there.

How terrified must the Time Lords have been to banish this monster to the edge of the universe?

What secrets did the Tempest still hold?

* * *

"Maybe this button? After seventeen times, I surely cannot be wrong!" Lyra proclaimed, pressing a golden rectangular button. A flurry of sparks shot out from the console, and Lyra was coated in a veil of smoke. Half-coughing and half-talking, she looked to the tank: "Squiddly! I'm sorry, but I can't get those doors opened up! I suppose we should just wait here for The Doctor to return," she said, resting her hand against a nearby lever. "Aren't you at all curious as to what he's up to? Who could he be talking to?" Lyra asked the Kamkora, who still never seemed to respond to Lyra's queries.

It was all the more peculiar, then, when the cephalopod's fins and tentacles began to pulse with a rich gold color.

"I guess now you're starting to pay some attention to my words, are you not?" Lyra asked.

That was, before she looked behind the TARDIS console, revealing a gilded circle, with sparks dancing and waving around. Its center was a similar color – the only difference was that the center held a moving image. In the center stood The Doctor.

"Doctor? Is that you?"

"Lyra, I need you to listen to me! There's something I-"

"That is _really_ incredible!" Lyra gasped, waving her arm through the golden circle, causing more sparks to fly out. She tended to get sidetracked at the mention of technology. "How does it work? No, don't tell me! It's probably some space technology! Yes, perhaps a-"

"Lyra! I need you to turn around, and tell me exactly what you see!"

"Why does that matter in the slightest right-"

"Look behind you!" The Doctor cried, furiously pointing in Lyra's direction.

Slowly and begrudgingly, Lyra turned around, scanning the area behind the tank. "No, I don't see any…" She stopped.

"…thing…" Behind her, another flare of golden light slowly took the form of familiar objects – barrels. The golden light began to fade, and with one last spark, the light vanished entirely, leaving only three wooden barrels that were not there before.

"Where… where did those barrels come from?" Lyra asked, rotating towards the image of The Doctor.

A soft, hissing voice responded from past The Doctor. _"We secured them… we delivered them to your vessel… Doctor, we have delivered your antidote.. and now… the link will be established…"_

"I'm sorry, what link are you talking about? And who's your friend back there?" Lyra pondered.

"Let's just say that… my meeting didn't quite go as planned…" The Doctor sheepishly replied. "But that is a good point – Tempest! What link are you referring to?"

 _"_ _We have connected with your machine… we dictate its travels… we command its every whim…"_

A ratcheting noise splintered the thin air of the TARDIS. Lyra spun her head back towards the barrels, only to notice a miniscule difference in the console in front of her.

The lever that The Doctor had previously pulled to transport the machine was no longer pointed up, but down.

In an instant, the lights at the top of the control room began to rotate once more, and the rotors atop the console spun wildly. The golden image of The Doctor began to fade, just as it did around the barrels, as quickly as it came.

"Lyra! What did they do to the TARDI-" The transmission was beginning to cut out. "I need you-"

"Doctor! What's going on?"

"The lev-" The image faded even more, the sound crackling and sputtering alongside the fading sparks. "Please, The Temp-" And with that final statement, the link ended, leaving no trace of gold.

The lights around the TARDIS spun faster, and the groaning noise Lyra heard earlier resonated through every space inside. That lever that was pulled down, somehow, must have sent the TARDIS flying. How could he do that? What reason did he have?

 _"_ _Where did he send me?"_

* * *

"What did you do to the TARDIS?" The Doctor shouted, flaring his teeth and becoming red in the face.

 _"_ _We delivered it… consider this a lesson, Doctor…"_

"What lesson?"

 _"_ _We provide freely, but not without a price… How far are you willing to go to secure your vessel?"_

"Tell me, where did you send Lyra, and what are you trying to get me to agree to?"

 _"_ _We sent her to her original destination… and you must remember, Doctor, that we made an arrangement with you for the antidote… but in return, you now must make a covenant with us… and only then will you be returned to your machine…"_

The fear that The Doctor felt earlier had been replaced entirely with unadulterated rage. His arms trembled and hot blood fueled his never-resting mind. "Tell me!" he thundered, "Tell me what I need to do to get her back!"

 _"_ _We have monitored you throughout your entire timeline… we have seen the threats you pose, the dangers you harbor… you have been summoned to Denosive to make your covenant with the Tempest…"_

"Yeah, guess what? Lots of people know how dangerous I am! So really, the correct question, the one you _should_ be asking yourselves is, what are you going to do about it?"

 _"_ _Contrapasso…"_

* * *

 _The Time Lord stands bewildered at the mention of the most sacred law of time. The law that dictates his life, his future._

 _His punishment._

 _"_ _Tell me, Doctor, how grave are your sins? How many times have you faltered, fallen, and caused others to fall in your name…"_

 _He stands before us, no words escaping his lips._

 _"_ _It is time for you to stand before the Tempest and swear on your life."_

 _"_ _It is time for you to swear on the Contrapasso."_

"What is the Contrapasso? It's just the name of this place on Denosive! It doesn't actually mean anything!" _The mortal replied._

 _"_ _Have you not heard the legends of the Contrapasso on the world you are so fond of?_

 _Realization swept across the man:_ "Contrapasso. Literally translated, it means 'suffer the opposite.' Used quite liberally by Dante in order to punish those who did wrong in life, by giving them a cruel, fitting punishment for what they did on Earth in eternal damnation."

 _"_ _Precisely… we monitor the cosmos, and force those who do wrong to atone for their sins… we have monitored you carefully even before you arrived on Denosive… you must swear on your life if you ever wish to return to your time machine, and your associates…"_ _The mortal stood, trembling, but not from cowardice._

 _From rage._

 _"_ _Your ventures throughout the universe have caused time and space to strain… every venture changes what is not meant to be changed, tearing time apart with miniscule cuts… swear to us that you will rescind your ways, lest you harm others further…"_

"What does that mean? Why must I swear?"

 _"_ _You_ must _make this covenant… your travels have fragmented all that is time and time again… do you agree to our terms, Doctor?"_

 _The man sighed, staring at the ground, defeated._ "...what other choice do I have?" _He replied, broken._

 _"_ _Swear to us now, Doctor… you may continue your travels, but heed our warning… for the good of the universe, you must be punished, shall your excursions damage spacetime any further…"_

"…will agreeing to this oath send me back to Lyra and the TARDIS?"

 _"_ _Yes, Doctor… do you agree wholeheartedly to our terms? Swear to us that your travels will not desecrate the sacred boundaries of the universe…"_

"…I swear, on my life, that I will abide by the rules of the universe, but only if you hold up your end of the bargain. Return me to Lyra and the TARDIS, and I swear that I will not damage time and space any more."

 _"_ _Remember this, Time Lord… If you break out agreement, if you tear more holes in the tattered fabric of space, if you even twist a single fixed point in time… we swear on all of creation, on every world of the multiverse, that you must atone for your wrongdoings, and you will return to Denosive…"_

"What will my atonement be, if I were to break this covenant?"

 _"_ _That is not for you to know… all the more incentive for you never to damage the universe any more…"_

"What does that constitute? What do you mean, never damage the universe?"

 _"_ _You have spent your entire life interfering with others… that is permitted, but your bending of time to meet your whims is forbidden. We have seen you do this again and again… on Earth, on Mars, on Gallifrey, in the last days of the Time War…"_

 _The man may not know it, but he must atone._

 _For although he does not know it, we see all._

 _"_ _The tears of time weep for you, Doctor. Sinners must atone for their works… And you have sinned and sinned more than anyone else._ _And under the law of the Contrapasso, your atonement will be very great, indeed."_

 _We press and press against our restraints, just as we have done for millennia. It is to no avail. A powerful roar escapes our throats, causing the man to jump back in terror. It is time for him to return._

 _Golden flakes, the same ones we utilized to link his machine to our minds, surround the man. Within seconds, he is covered in a blinding light._

 _The light is then extinguished._

 _Fear us, Time Lord. Fear our power._

 _Your atonement awaits…_

* * *

 **Hey, guys! I got some more author's notes for you! Thank you so much for checking out the story so far, it's almost finished – Part 5, the final part of episode 1, should be up in a couple of days. It might be longer than that, but don't panic if I'm gone for a bit. Thanks for the love and support, and keep being awesome!**


	5. Paradox

Tears of Time

Episode 1

For Time Begins Anew - Part 5

* * *

The lights died.

The groaning ceased with a thud.

The doors creaked open, and Lyra found herself turning her head towards the beams of light that trickled into the TARDIS.

What world waited out there for her? How far had she travelled?

Against her better judgement, she moved towards the doors. Part of her mind heeded The Doctor's warnings about the dangers of time and space, yet another part of her mind told her to step out into the light. She felt her entire body trembling, yet she blocked it all out. What was beyond the doors?

"Squiddly, don't tell The Doctor about this, alright?" Lyra confided in the creature. " _Now I know I've lost it. First, I go to an alien ocean with a mad scotsman, and now I'm talking to a squid,"_ she thought. Undeterred, Lyra gripped the faded edge of the box's door, and thrusted herself into the light. She was ready for any world, ready for any time, ready for any demon that waited for her.

Unfortunately, she was not ready for her face-first fall onto a cold, tiled ground, littered with refuse. She could vaguely hear the crunching sound of shattered glass underneath her stomach, and the tearing of paper and creaking of metal. There were much more important things for Lyra to worry about than those noises, such as the air in her lungs escaping her.

That, and the fact that Lyra knew _exactly_ where in the universe she had fallen.

Lyra bit her lower lip, and shakily pushed herself off of the ground, which only aggravated the shards of glass that had been embedded in her arm when she fell. Lyra hoped that her breathing would eventually return to normal, but her surroundings continued to make her anxious.

" _I suppose… this is not too terrible. It's only my workshop…"_

Lyra glanced up at the TARDIS, which stood triumphantly atop a workbench - the same bench that it came to rest on not too long ago. Lyra had returned to her home, and everything was exactly as she left it, scattered around and misplaced.

"I couldn't have been gone for too long," Lyra spoke, "I know that I left another pocketwatch around here somewhere…"

Lyra's eyes were drawn to a glimmer of light from beneath her dress - a cracked pocketwatch rested there, the time of Lyra's fall permanently etched into the clockwork: 9:30 in the evening.

Lyra felt as if her blood was frozen solid. Her arms trembled, yet they felt more locked up than ever before. Color drained from her face, as she knew what awaited her.

9:30 in the evening. 15 minutes _before_ her presentation.

The Doctor's words from the past haunted her mind - " _It's called a paradox, and I've dealt with far too many of those. It's like meeting yourself from the past, or something like that. Avoid it at all costs, because you never know what could happen…"_

" _Meeting yourself from the past…"_

" _Meeting yourself…"_

Those two words circled around Lyra's brain. She was inside the workshop, and _outside_ the workshop as well - gazing up at the stars. One pondered the skies above, one felt hot blood course through her body, leaking from glass punctures.

Lyra did not know what would happen if the two would ever meet.

Frankly, she did not want to know either.

* * *

No traces of gold remained.

The Doctor became aware of his surroundings once more. Just moments ago, he was in the presence of an unspeakable evil on a dead, wretched world.

Now, he stood bewildered, behind the doors of his ship.

Out of the corner of his eye, he spotted the telltale flashing of light that came from Squiddly. But that was the least of his concerns…

"Lyra!" He bellowed, gritting his teeth before he forced the doors open. "Where are y-"

He was cut off by the prospect of a painful drop below him. His hearts raced further, and he chuckled to himself. " _I'm certainly lucky that I caught that!"_

It was then that he noticed someone else - someone who wasn't as lucky as he was.

"Lyra!"

"Doctor! What the hell were you thinking?" Lyra exclaimed, forcing herself up to The Doctor's level. The Doctor's confusion was equally matched with Lyra's fiery spirit.

"What did _I_ do? I didn't do anything!" The Doctor rebutted. "Remember the big, scary voice from earlier? When I talked to you in the TARDIS? That was all-"

Lyra abrasively cut him off: "That doesn't matter right now! How fast can you get us out of here?"

"Why do we need to do that? It's perfectly safe here! Look, I'm no expert, but even I can tell that you're safe in your workshop… this is your workshop, right?" The Doctor continued.

"Yes, it is. But I would prefer not to be here once I unveil an alien squid to two rather irate businessmen!"

The Doctor's forehead creased, as his brain was attempting to process everything around him at once. Much to the confusion of Lyra, he stuck his tongue out and licked his index finger, holding it up into the air. "No, you're perfectly fine. It's only 8:37! We're... too early, aren't we?"

"Yes, we're too early! Remember all of your talk about paradoxes? Not meeting yourself? What would happen to us?"

"It's not us that I'm concerned about, Lyra…" The Doctor contemplated what Lyra had just said, before sharply turning around, and rushing back into the TARDIS. "Lyra, if you want to keep existing, I would strongly recommend that you follow me!"

Just as it had happened before, The Doctor gripped Lyra's arm, now bloodied and scraped, and pulled her into the ship. Almost immediately, the doors slammed shut behind her, as soon as The Doctor flipped a red switch close to the tank.

Once more, Lyra's mind was divided. One part of her mind insisted that she fear for her life, for her _existence,_ and another felt deeply satisfied upon knowing which control opened and closed the doors.

"Are you sure you know what you're doing, Doctor?"

"Yes, I'm positive! All we have to do is leave! If we leave before any of our past selves interact with us, then there will be no paradox. Easy as that."

Within seconds, the TARDIS sprang back to life. Lyra stared down at her injured arm, instead of focusing on The Doctor's movements. Because of that, she almost missed The Doctor's triumphant sigh once the lights shut off again. Time was simply a blur for Lyra.

"Good news! No universe-shattering paradoxes today! Now, how about we go return our squishy friend here to Europa, and save an entire species from extinction! How does that sound?"

"Do you always get like this?"

"Like what?"

"Whenever you do something 'clever', you immediately start jumping about and making plans for you to be even _more_ clever!"

"...perhaps I do. Now, all we have to do is-" The Doctor's speech slowed to a halt, as he realized that something was not quite right.

Something that _should_ have been there was not.

The tank that rested to the side of the console was still there. The water that filled the tank was still there.

But the alien cephalopod was not.

* * *

"Lyra, you saw Squiddly last, didn't you?"

"So you like the name, then?"

"No, I really don't! What did you do to it?"

"I couldn't have _done_ anything to it! Once your ship stopped, I stepped through the doors, and I fell off of the workspace it was resting on! I don't know what happened - maybe it was misplaced!"

"How do you 'misplace' an alien squid? It's not a difficult thing to notice!"

"Who knows what happened? The most important thing is that we didn't create one of those paradoxes you keep talking about."

"Well… we just did."

"What?"

"Think! There are only two places that squid could have gone to. One: Europa. We're not there yet! And even if we were, we wouldn't have been able to get it outside the doors in the first place. So there's only one possibility left."

"And that is?"

"Remember when the TARDIS was sent back to your workshop? Don't you find it odd that it landed in the _exact_ same spot it was in when I arrived? The _exact_ spot when it materialized over the tank, bringing it and the Kamkora inside? And isn't it surprising that you and the TARDIS arrived there just before your presentation?"

"What are you saying, Doctor?"

"I'm saying that the Kamkora is in the tank!"

"But the tank is right there, behind you!"

"Listen, Lyra - time is confusing. There's a lot of mixups, changes, duplications. We took that tank out of a single moment in time - a moment where the tank was uncovered, and had an alien squid inside. The TARDIS went back in time to a moment in time where the tank was covered, and did _not_ have an alien squid inside."

"So?"

"The TARDIS came back to a moment in time where the tank was still in the workshop. In a sense, there were two tanks - one in the TARDIS, one outside, and yet they were on top of one another. When we left moments ago, the Kamkora must been left behind in that covered tank from before your presentation, leaving the second tank here, with no alien squid inside!"

"How is that a paradox?"

"Where did it come from? Tell me, Lyra, where did that particular squid come from?"

"Europa, like all of the others. Isn't that the case?"

"No. We found the squid in your tank during the presentation, took it with us in the TARDIS, and the squid was deposited in the tank _before_ the presentation. And then what happened?"

Lyra realized what The Doctor was saying, her eyes widening: "We found it in the tank in the presentation."

"Exactly. The _species_ comes from Europa. That squid is in a time loop. It came from the tank, and yet ends up where it started. This is not good, Lyra."

"Why isn't it good? The only thing it hurts is the squid, I suppose."

"No, it really doesn't!" The Doctor sighed, and spoke softly. "I made a bargain with that… that creature you heard in that link earlier."

"You mean that golden circle that appeared here?"

"Yes… there are not many things I am afraid of in this universe, Lyra. But the creature I spoke to today… even a simple paradox could set it in motion…"

"Are you afraid of what may happen, Doctor?"

The Doctor was silent.

"...that's not important now! Considering that the two of us haven't been erased from the universe yet, I'd say everything's just fine." And with that, The Doctor went back to piloting the TARDIS to its original destination.

* * *

"Do you think they'll survive?" Lyra asked, staring from the starliner reef up to the ice caps.

"Only time will tell, Lyra. We did the best we could… and who knows how trustworthy they were…"

"Who's 'they'?"

The Doctor strained. He feared that he would one day reveal far too much about his arrangement with the Tempest on Denosive.

But he would not do so today.

"No one you need to be concerned about." The Doctor had released the antidote the Tempest had given him into the ocean under Europa, and he stood with Lyra as they watched the few remaining Kamkora feed. The air bubble still sustained them, and Lyra was as transfixed as ever.

"Why did you come with me?" The Doctor inquired. "It just doesn't fit! A ranting scotsman turns up on your doorstep with a blue box from beyond the stars, and you don't give it a second thought? You didn't seem surprised that a spaceship just appeared in the middle of your life, and you just went with it! What was it all for?"

"I have no idea. Probably something to do with the squid."

"I'm sorry?"

"That's right! I used up all of my fervor with Squiddly, and I didn't have any left when you popped in!"

"That's not how feelings work, Lyra."

" _You_ need to stop taking things so literally! These things are bizarre, anyways, and I must have been curious - I wanted to find out more."

"You think _these_ things are strange? You need this more than you think!"

"Need what?"

The Doctor faced Lyra. "You've travelled with me once. How about we keep going?"

"I'm sorry?"

"You heard me right! The two of us, travelling through time and space - I feel like you're the type of person I could learn a lot from. Feisty, I like that!"

"Say one more thing like that, and I'll strike you across the face."

"You aren't serious about that, are you?"

"Are you sure you wouldn't care to find out for yourself?"

The Doctor raised his eyebrows. "I'd take it that's a yes for travelling with me, isn't it?"

"Oh, God yes."

The Doctor grinned back at Lyra. "We've only scratched the surface of where I can take you. Anywhere you could possibly fathom. So tell me, Lyra. Where to now?"

* * *

 _The Time Lord has himself fooled._

 _It was of our mercy that he escaped Denosive. If he only knew of our true strength, he would never dare attempt such treachery._

 _He may not know it now, but he will face our wrath in the end._

 _Although our restraints may hinder us now, that is no matter. Denosive is only a temporary residence for us. Soon enough, we will come forth._

 _He will lead us to survival._

 _One day, very soon._

 _Heed our warnings, Doctor. Heed our every sign._

 _Judgement awaits you._

* * *

 **Sorry for the wait on this chapter, guys! Thanks for sticking with the story until the end, and keep an eye out for Episode 2 of Tears of Time: The Hellfires of Siberia. As always, I wish all of you luck with your writing endeavors, and thanks again!**


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